[gmx-users] FEP for amino acid mutations

Matteo De Chiara matnamo at gmail.com
Mon Jun 21 17:13:53 CEST 2010

Dear Gromacs user,

Still another problem...

How can I manage the mutation upon a Trp?
The mutation ALA-GLY does not cause any problem but the trasformation
TRP-ALA seems uneasy.

The Segmentation Fault error occurs suddenly I try to run the mdrun
with lambda=1, with lambda=0.99 it take 6 step before to crash while
if I start with lambda=0 it seems to work.
So, I was thinking that it could be because the whole Trp rings, which
loses lennard-jones interaction and charge, have still all its mass
and this mass are connected on a single HB of the final alanine ( I'm
using tha amber all-atom force field) that was the CG in the initial
Could it be?
Can how manage it somehow?

Furthermore, if I change an aromatic residue in some long-sidechain
amino acid how can I manage the dihedral and the bonds? I think I
cannot let a bond disappear, for example if I try to transform a PHE
in a LEU...

Thank you for any hint you could give me!


> Date: Wed, 16 Jun 2010 15:17:30 +0200
> From: Matteo De Chiara <matnamo at gmail.com>
> Subject: Re: [gmx-users] FEP for amino acid mutations.
> To: gmx-users at gromacs.org
> Message-ID:
>        <AANLkTikBuM3hTGnGlS6mO-cjl-BuEhPGEIfDRHVk3q1o at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> Thank you!
> I tried to change from Ala to Gly in aqueous environment and seems to
> have worked well. Now I will try to change a Trp, the amino acid  I
> have to apply the real mutation.
> matteo
>> Message: 5
>> Date: Tue, 15 Jun 2010 08:53:25 +1000
>> From: "Dallas B. Warren" <Dallas.Warren at pharm.monash.edu.au>
>> Subject: RE: [gmx-users] FEP for amino acid mutations.
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID:
>>        <89907EA1DCFB7548A431C13A270F9DD50AD84269 at prk-exch-01.vcp.local>
>> Content-Type: text/plain; charset=us-ascii
>> I would make a new residue in the .rtp file.
>> Catch ya,
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3010
>> dallas.warren at pharm.monash.edu.au
>> +61 3 9903 9167
>> ---------------------------------
>> When the only tool you own is a hammer, every problem begins to resemble
>> a nail.
>>> -----Original Message-----
>>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
>>> bounces at gromacs.org] On Behalf Of Matteo De Chiara
>>> Sent: Monday, 14 June 2010 8:05 PM
>>> To: gmx-users at gromacs.org
>>> Subject: [gmx-users] FEP for amino acid mutations.
>>> Dear GROMACS users,
>>> I would like to perform a FEP calculation mutating a residue outside
>>> the active site of a protein.
>>> I was wondering if I have to create a .itp file for the mutation or it
>>> is possible to modify the .rtp file ( adding the state B parameter to
>>> the amino acid I would like to change). Of course, in this case, I
>>> will create a new amino acid type identical to the one I would like to
>>> mutate in order to act only on the amino acid in a specific position.
>>> Thanks for your help!
>>> matteo

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